SAXSdb — 10ay

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1. Structure Basics

entry_id	10ay
deposition_date	2026-01-09
title	Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961
keywords	FOCAD, ribosome, PELO, ubiquitin, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	60.82 Å
rg_electron	61.80 Å
i0	1111920000.00
molecular_weight	286610.0 kDa
excluded_volume	361790 Å³
envelope_volume	517700 Å³
shell_volume	75220 Å³
envelope_diameter	209.4 Å
shell_rg	54.30 Å
envelope_rg	60.93 Å
shape_rg	61.82 Å
total_rg	61.51 Å
total_atoms	40391
n_residues	2524
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	191.9 Å
rg_real	61.72 Å
rg_real_error	2.11 Å
i0_real	1.1120e+09
i0_real_error	2.4200e+07
rg_reciprocal	59.98 Å
i0_reciprocal	1109000000.0000
total_estimate	0.7532
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.3 Å
skewness	0.512
kurtosis	-0.704
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	103200000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.665; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.793; Smooth: 0.001

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	HBS1-like protein
formula_weight	22947.0 kDa
ec_number	3.6.5.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	40391

GKPPQRSIDKPFRLCVSDVFKDQGSGFCITGKIEAGYIQTGDRLLAMPPNETCTVKGITLHDEPVDWAAAGDHVSLTLVGMDIIKINVGCIFCGPKVPIKACTRFRARILIFNIEIPITKGFPVLLHYQTVSEPAVIKRLISVLNKSTGEVTKKKPKFLTKGQNALVELQTQRPIALELYKDFKELGRFMLRYGGSTIAAGVVTEIKE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Protein cereblon
formula_weight	46378.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

GEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	DNA damage-binding protein 1
formula_weight	127097.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 non-polymer

description	N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea
formula_weight	539.6 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.90 Å
resolution_method	—
num_particles	669259

fit	/app/data/saxs_computation/0a/10ay/10ay.fit
pddf	/app/data/pr_computation/0a/10ay/10ay.pr.out
profile	/app/data/saxs_computation/0a/10ay/10ay.dat

Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)